Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
Microglia
MeSH Description
The third type of glial cell, along with astrocytes and oligodendrocytes (which together form the macroglia). Microglia vary in appearance depending on developmental stage, functional state, and anatomical location; subtype terms include ramified, perivascular, ameboid, resting, and activated. Microglia clearly are capable of phagocytosis and play an important role in a wide spectrum of neuropathologies. They have also been suggested to act in several other roles including in secretion (e.g., of cytokines and neural growth factors), in immunological processing (e.g., antigen presentation), and in central nervous system development and remodeling.

Attributes by original data submitter

Sample

source_name
Microglia
cell line
C20
chip antibody
CTCF (Cell Signaling, #3418)
treatment
untreated

Sequenced DNA Library

library_name
GSM6824679
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10x10^6 million microglia cells were fixed with 1% formaldehyde/PBS followed by quenching with 0.125 M glycine. After washing with cold PBS, pellet was resuspended in swelling buffer, cytosol was removed and nuclei sonicated. Lysates were cleared and 2-8 microgram of chromatin were incubated with corresponding amounts of antibody overnight at 4°C. The next day, chromatin was captured with Protein A/G beads, washed and eluted with TE buffer, 1% SDS, 100 mM NaCl. 0.5 mg/ml Proteinase K were added, and samples were incubated for 2 h at 55°C and overnight at 65°C. The next day, RNA was digested. Supernatant was removed from the magnetic beads and DNA was purified with AMpure beads XP clean up according to manufacturer's instructions. ChIP libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (NEB) according to manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
11736356
Reads aligned (%)
98.6
Duplicates removed (%)
6.2
Number of peaks
438 (qval < 1E-05)

hg19

Number of total reads
11736356
Reads aligned (%)
97.7
Duplicates removed (%)
6.4
Number of peaks
315 (qval < 1E-05)

Base call quality data from DBCLS SRA